If making the acorn squash bowls, preheat oven to 375°F. Slice about an inch off stem ends of squash and scrape out seeds and strings. Slice a bit off blossom ends so the bowls can stand up. Drizzle with olive oil and place in a lightly oiled baking dish. Bake for 30 to 40 minutes or until insides are fork tender.
To make the soup: Melt butter in a large pot over medium-high heat. Sauté butternut squash, leeks, and carrots until soft, 8 to 10 minutes. Stir in the diced apples, thyme, salt, pepper, and chicken stock. Bring to a boil, then reduce heat, cover, and simmer 20 to 30 minutes until squash is tender.
Remove soup from heat, add milk or cream, and process with a blender until smooth. Gently reheat before serving.
If serving in acorn squash bowls, make sure to scoop into the flesh to enjoy it as part of the soup.
Garnish with bacon, sage leaves, and a drizzle of extra virgin olive oil.